Fix resolution of params in resolved config text (#7072)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>

Author: jorgee

modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy

@@ -406,7 +406,7 @@ class CmdRun extends CmdBase implements HubOptions {
         final isTowerEnabled = config.navigate('tower.enabled') as Boolean
         final isDataEnabled = config.navigate("lineage.enabled") as Boolean
         if( isTowerEnabled || isDataEnabled || log.isTraceEnabled() )
-            runner.session.resolvedConfig = ConfigBuilder.resolveConfig(scriptFile.parent, this)
+            runner.session.resolvedConfig = ConfigBuilder.resolveConfig(scriptFile.parent, this, cliParams)
         // note config files are collected during the build process
         // this line should be after `ConfigBuilder#build`
         runner.session.configFiles = builder.parsedConfigFiles

modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy

@@ -919,13 +919,14 @@ class ConfigBuilder {
         }
     }
 
-    static String resolveConfig(Path baseDir, CmdRun cmdRun) {
+    static String resolveConfig(Path baseDir, CmdRun cmdRun, Map cliParams) {
 
         final config = new ConfigBuilder()
                 .setShowClosures(true)
                 .setStripSecrets(true)
                 .setOptions(cmdRun.launcher.options)
                 .setCmdRun(cmdRun)
+                .setCliParams(cliParams)
                 .setBaseDir(baseDir)
                 .buildConfigObject()
 

modules/nextflow/src/test/groovy/nextflow/config/ConfigBuilderTest.groovy

@@ -2410,9 +2410,9 @@ class ConfigBuilderTest extends Specification {
 
     def 'should return parsed config' () {
         given:
-        def cmd = new CmdRun(profile: 'first', withTower: 'http://foo.com', launcher: new Launcher())
         def base = Files.createTempDirectory('test')
-        base.resolve('nextflow.config').text = '''
+        def configFile = base.resolve('nextflow.config')
+        configFile.text = '''
         profiles {
             first {
                 params {
@@ -2422,25 +2422,31 @@ class ConfigBuilderTest extends Specification {
                 process {
                     executor = { 'local' }
                 }
+                outputDir = params.outdir
             }
             second {
                 params.none = 'Blah'
             }
         }
         '''
         when:
-        def txt = ConfigBuilder.resolveConfig(base, cmd)
+        def opt = new CliOptions(config: [configFile.toFile().canonicalPath])
+        def cmd = new CmdRun(profile: 'first', withTower: 'http://foo.com', launcher: new Launcher(options: opt))
+        def cliParams = [foo: 'Hola', outdir: 'output_folder']
+        def txt = ConfigBuilder.resolveConfig(base, cmd, cliParams)
         then:
         txt == '''\
             params {
-               foo = 'Hello world'
+               foo = 'Hola'
                awsKey = '[secret]'
+               outdir = 'output_folder'
             }
             
             process {
                executor = { 'local' }
             }
 
+            outputDir = 'output_folder'
             workDir = 'work'
             
             tower {